Diagnostic work in SSMSE

This is all of the code that uses r4ss to pull individual runs from an SSMSE folder and looks closer at data that is not extracted in the summary function. It was starting to slow down my quarto document so I have moved it to this quarto document.

Pull data from SS runs

This chunk takes a while to run and pulls the ss_output data from all iterations and all scenarios, it only saves the data that is listed, so selectivity, catage, batage, natage, and new CPUE indexes.

Selectivity Exploration

Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

natage

batage

catage

CPUE

Selectivity Exploration Disc

Retention Exploration

Ro Exploration

Extracted the R0 from SR_LN_R0 from the summary$scalar.